Reverse Flash is from the future, and thus is BOUND by the future.
RF knows what has happened and what is going to happen and in his own twisted way, he is playing the role of villain to get Barry to step it up and become and hero.
Every hero NEEDS a villain. Or two or three.
Wells/Zoom/Reverse Flash has set out to ensure that Barry does become the Flash by being the killer of his mother, he built the particle accelerator and knowingly set it to fail so that Barry and others would become super powered. Reverse Flash is easily one step ahead of Barry in terms of planning and knowledge and could kill Barry with ease, but that is not his end goal.
Unless Barry in 2024 makes the big sacrifice to stop the Crisis on Infinite Earths, then Reverse Flash's future will be negated.
So in essence, RF is out to preserve himself and his future and in order to do that he must fulfill the past by being Barry's villain. RF knows what is coming as far as future fights with Barry and will play his role as history has already dictated, even if there is a point where Barry catches and contains Reverse Flash or even kills him, that will still be per the script set by history itself.
Also given that RF is a time traveler, killing him now wouldn't matter since we don't know what future events he will still show up in due to his time traveling.